alpha.compare: Compare multiple alpha diversity indexes between groups

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

Description

This function calculates average of alpha diversity indexes for a specific rarefaction depth, standardize diversity indexes and compare between groups using linear/linear mixed effect model and adjust for covariates.

Usage

alpha.compare(
  datlist,
  depth,
  mapfile,
  mapsampleid,
  comvar,
  adjustvar,
  personid = "personid",
  longitudinal = "yes",
  age.limit = 1e+06,
  standardize = FALSE
)

Arguments

datlist	the list of your dataframe.
depth	the rarefaction depth of choice. Depth can be "max" (highest depth) or an order (number) of the depth in the list generated by alpha_rarefaction.py
mapfile	mapping file
mapsampleid	sample id in the mapping file
comvar	variable for comparison
adjustvar	variables that need to be adjusted in the model
personid	name of variable for person id. Default is "personid" (applicable when longitudinal="yes").
longitudinal	longitudinal data or one time data. Options are c("yes","no"). Default is "yes".
age.limit	age upper limit for included samples. Default is 1000000 months (~no upper limit).
standardize	standardization of diversity indexes before comparison or not. Default is FALSE.

Value

list of comparison result matrices and mean diversity of all indexes for each samples (with or without standardization)

Examples

data(alphadat)
data(covar.rm)
covar.rm$sampleid<-tolower(covar.rm$sampleid)
#comparison of standardized alpha diversity indexes between genders adjusting for
#breastfeeding and infant age at sample collection in infants <=6 months of age
alphacom<-alpha.compare(datlist=alphadat,depth=3,mapfile=covar.rm,
mapsampleid="sampleid", comvar="gender",adjustvar=c("age.sample","bf"),
longitudinal="yes", age.limit=6,standardize=TRUE)
alphacom$alphasum[,1:5]

Example output

Loading required package: gamlss
Loading required package: splines
Loading required package: gamlss.data

Attaching package: ‘gamlss.data’

The following object is masked from ‘package:datasets’:

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.2-0  ********** 
For more on GAMLSS look at https://www.gamlss.com/
Type gamlssNews() to see new features/changes/bug fixes.

There were 50 or more warnings (use warnings() to see the first 50)
                id Estimate.genderMale Std. Error.genderMale t value.genderMale
1            chao1         -0.06535198             0.1502276         -0.4350197
2 observed_species         -0.14283545             0.1363228         -1.0477741
3    pd_whole_tree         -0.13246866             0.1452980         -0.9117031
4          shannon         -0.44008064             0.1993104         -2.2080165
  Pr(>|t|).genderMale
1          0.66354814
2          0.29474270
3          0.36192504
4          0.02724312

metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.